hpc-beeflow 0.1.11.dev2__tar.gz → 0.1.11.dev4__tar.gz

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/PKG-INFO

@@ -1,7 +1,8 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.1
 Name: hpc-beeflow
-Version: 0.1.11.dev2
+Version: 0.1.11.dev4
 Summary: A software package for containerizing HPC applications and managing job workflows
+Home-page: https://github.com/lanl/BEE
 Keywords: bee,hpc,workflow,cluster,computing
 Author: BEE-LANL Dev Team
 Author-email: bee-dev@lanl.gov
@@ -19,7 +20,6 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: System :: Clustering
@@ -49,6 +49,7 @@ Requires-Dist: python-heatclient (>=3.1.0,<4.0.0) ; extra == "cloud-extras"
 Requires-Dist: python-openstackclient (>=6.0.0,<7.0.0) ; extra == "cloud-extras"
 Requires-Dist: requests (>=2.32.3,<3.0.0)
 Requires-Dist: requests-unixsocket2 (>=0.4.2,<0.5.0)
+Requires-Dist: tabulate (>=0.9.0,<0.10.0)
 Requires-Dist: typer (>=0.5.0,<0.6.0)
 Requires-Dist: uvicorn (==0.27.1)
 Project-URL: Repository, https://github.com/lanl/BEE
@@ -89,11 +90,27 @@ Containers provide many benefits:
 BEE Sites
 =========
 
-* Documentation: `https://lanl.github.io/BEE/ <https://lanl.github.io/BEE/>`_
-
 * Github: `https://github.com/lanl/BEE <https://github.com/lanl/BEE>`_
 
 
+* PyPi: `https://pypi.org/project/hpc-beeflow/ <https://pypi.org/project/hpc-beeflow/>`_
+
+.. list-table:: 
+   :header-rows: 1
+   :widths: 20 25 55
+
+   * - Purpose
+     - Git Tag
+     - Documentation
+
+   * - Stable release
+     - ``0.1.10``
+     - `https://lanl.github.io/BEE/ <https://lanl.github.io/BEE/>`__
+   * - Pre-release
+     - ``0.1.11dev3``
+     - `https://lanl.github.io/BEE/0.1.11dev3/ <https://lanl.github.io/BEE/0.1.11dev3/>`__
+
+
 Contact
 =======
 
@@ -114,6 +131,7 @@ Contributors:
 * Ragini Gupta - `raginigupta6 <https://github.com/raginigupta6>`_
 * Aaron R Hall - `arhall0 <https://github.com/arhall0>`_
 * Leah Howell - `Leahh02 <https://github.com/Leahh02>`_
+* Lilikoi Latimer - `lilikoi-l <https://github.com/lilikoi-l>`_
 * Andres Quan - `aquan9 <https://github.com/aquan9>`_
 * Quincy Wofford - `qwofford <https://github.com/qwofford>`_
 * Tim Randles - `trandles-lanl <https://github.com/trandles-lanl>`_

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/README.rst

@@ -33,11 +33,27 @@ Containers provide many benefits:
 BEE Sites
 =========
 
-* Documentation: `https://lanl.github.io/BEE/ <https://lanl.github.io/BEE/>`_
-
 * Github: `https://github.com/lanl/BEE <https://github.com/lanl/BEE>`_
 
 
+* PyPi: `https://pypi.org/project/hpc-beeflow/ <https://pypi.org/project/hpc-beeflow/>`_
+
+.. list-table:: 
+   :header-rows: 1
+   :widths: 20 25 55
+
+   * - Purpose
+     - Git Tag
+     - Documentation
+
+   * - Stable release
+     - ``0.1.10``
+     - `https://lanl.github.io/BEE/ <https://lanl.github.io/BEE/>`__
+   * - Pre-release
+     - ``0.1.11dev3``
+     - `https://lanl.github.io/BEE/0.1.11dev3/ <https://lanl.github.io/BEE/0.1.11dev3/>`__
+
+
 Contact
 =======
 
@@ -58,6 +74,7 @@ Contributors:
 * Ragini Gupta - `raginigupta6 <https://github.com/raginigupta6>`_
 * Aaron R Hall - `arhall0 <https://github.com/arhall0>`_
 * Leah Howell - `Leahh02 <https://github.com/Leahh02>`_
+* Lilikoi Latimer - `lilikoi-l <https://github.com/lilikoi-l>`_
 * Andres Quan - `aquan9 <https://github.com/aquan9>`_
 * Quincy Wofford - `qwofford <https://github.com/qwofford>`_
 * Tim Randles - `trandles-lanl <https://github.com/trandles-lanl>`_

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/client/bee_client.py

@@ -27,6 +27,7 @@ import requests
 import typer
 import yaml
 
+from tabulate import tabulate
 from beeflow.common import config_driver
 from beeflow.common.cli import NaturalOrderGroup
 from beeflow.common.connection import Connection
@@ -572,12 +573,35 @@ def query(wf_id: str = typer.Argument(..., callback=match_short_id)):
     tasks_status = resp.json()['tasks_status']
     wf_status = resp.json()['wf_status']
     typer.echo(wf_status)
-    for _task_id, task_name, task_state in tasks_status:
+
+    scheduler = config_driver.BeeConfig.get('DEFAULT','workload_scheduler').lower()
+    if scheduler == 'slurm' and config_driver.BeeConfig.get('slurm','use_commands'):
+        section = 'slurm command attributes'
+    elif scheduler == 'flux':
+        section = 'flux attributes'
+    else:
+        section= 'slurm attributes'
+
+    attrs = config_driver.BeeConfig.get(section, 'attributes')
+    logging.info(attrs)
+    if isinstance(attrs,str):
+        attrs = [attr.strip() for attr in attrs.split(',') if attr.strip()]
+
+    attr_data=[]
+    for _task_id, task_name, task_state,metadata in tasks_status:
         if wf_status == 'No Start':
             typer.echo(f'{task_name}')
-        else:
-            typer.echo(f'{task_name}--{task_state}')
-
+            continue
+
+        output_fields=[task_name,task_state]
+        for attr in attrs:
+            value = metadata.get(attr)
+            if value is not None:
+                output_fields.append(str(value))
+        attr_data.append(output_fields)
+    headers = ['task_name','task_state'] + attrs
+    if attr_data:
+        typer.echo(tabulate(attr_data,headers=headers,tablefmt="fancy grid"))
     logging.info('Query workflow:  {resp.text}')
     return wf_status, tasks_status
 
@@ -739,14 +763,21 @@ def dag(wf_id: str = typer.Argument(..., callback=match_short_id),
         typer.secho("Workflow has been archived. All new DAGs will look the same as the one "
                     "in the archive directory.",
                     fg=typer.colors.MAGENTA)
-        wf_utils.export_dag(wf_id, output_dir, graphmls_dir, no_dag_dir)
+        dot_avail = wf_utils.export_dag(wf_id, output_dir, graphmls_dir, no_dag_dir)
     else:
         wf_dir = wf_utils.get_workflow_dir(wf_id)
         graphmls_dir = wf_dir + '/graphmls'
         os.makedirs(graphmls_dir, exist_ok=True)
-        wf_utils.export_dag(wf_id, output_dir, graphmls_dir, no_dag_dir, wf_dir)
-    typer.secho(f"DAG for workflow {_short_id(wf_id)} has been exported successfully.",
-                fg=typer.colors.GREEN)
+        dot_avail = wf_utils.export_dag(wf_id, output_dir, graphmls_dir, no_dag_dir, wf_dir)
+    if dot_avail:
+        typer.secho(f"DAG for workflow {_short_id(wf_id)} has been exported successfully.",
+                    fg=typer.colors.GREEN)
+    else:
+        typer.secho(
+            f"GraphML for workflow {_short_id(wf_id)} has been exported successfully."
+            "(Graphviz not found, so no rendered DAG was produced.)",
+            fg=typer.colors.GREEN
+        )
 
 
 @app.callback(invoke_without_command=True)

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/client/core.py

@@ -18,7 +18,7 @@ import datetime
 import time
 import importlib.metadata
 from pathlib import Path
-
+from configparser import ConfigParser
 import daemon
 import typer
 
@@ -35,6 +35,45 @@ from beeflow.common.deps import container_manager
 from beeflow.common.deps import neo4j_manager
 from beeflow.common.deps import redis_manager
 
+from beeflow.common.config_driver import USERCONFIG_FILE
+
+def patch_attribute_section():
+    """Replace the default attributes in the config file based on the scheduler"""
+    if not os.path.exists(USERCONFIG_FILE):
+        return
+
+    config= ConfigParser()
+    with open(USERCONFIG_FILE, encoding='utf-8') as f:
+        config.read_file(f)
+
+    sched = config.get('DEFAULT', 'workload_scheduler', fallback='Slurm')
+    if sched == 'Flux':
+        section = 'flux attributes'
+        default_attrs = 'queue,runtime,nodelist'
+    elif sched == 'Slurm':
+        use_cmds = config.get('slurm', 'use_commands', fallback='True').strip().lower() == 'true'
+        if use_cmds:
+            section = 'slurm command attributes'
+            default_attrs = 'Partition,RunTime,NodeList'
+        else:
+            section = 'slurm attributes'
+            default_attrs = 'partition,nodes'
+    else:
+        return
+
+    if not config.has_section(section):
+        config.add_section(section)
+        config.set(section, 'attributes', default_attrs)
+    else:
+        cur_attrs = config.get(section, 'attributes', fallback='').strip()
+        if not cur_attrs:
+            config.set(section, 'attributes', default_attrs)
+        else:
+            return
+
+    with open(USERCONFIG_FILE, 'w', encoding='utf-8') as f:
+        config.write(f)
+
 
 REPO_PATH = Path(*Path(__file__).parts[:-3])
 
@@ -344,6 +383,9 @@ class Beeflow:
     def loop(self):
         """Run the main loop."""
         print(f'Running on {socket.gethostname()}')
+        # Check for Graphviz:
+        if not shutil.which("dot"):
+            print('Graphviz was not found on PATH.')
         self.mgr.run(self.base_components)
         with cli_connection.server(paths.beeflow_socket()) as server:
             while not self.quit:
@@ -395,7 +437,6 @@ def daemonize(mgr, base_components):
                               umask=0o002):
         Beeflow(mgr, base_components).loop()
 
-
 app = typer.Typer(no_args_is_help=True)
 
 
@@ -405,6 +446,7 @@ def start(foreground: bool = typer.Option(False, '--foreground', '-F',
           '-B', help='allow to run on a backend node'), remote: bool = typer.Option(False, 
           '--remote', '-R', help='allow remote connection')):
     """Start all BEE components."""
+    patch_attribute_section()
     start_hn = socket.gethostname()  # hostname when beeflow starts
     if bee_client.get_hostname() == "" and bee_client.check_backend_status() == "":
         bee_client.setup_hostname(start_hn)  # add to client db
@@ -427,6 +469,7 @@ def start(foreground: bool = typer.Option(False, '--foreground', '-F',
     sock_path = paths.beeflow_socket()
     if bc.get('DEFAULT', 'workload_scheduler') == 'Slurm' and not need_slurmrestd():
         warn('Not using slurmrestd. Command-line interface will be used.')
+
     # Note: there is a possible race condition here, however unlikely
     if os.path.exists(sock_path):
         # Try to contact for a status

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/common/build/container_drivers.py

@@ -45,47 +45,53 @@ class CharliecloudBuildDriver(ContainerBuildDriver):
         :param task: the task to build for
         :type task: Task
         """
-        # Store build container archive pased on config file or relative to bee_workdir if not set.
-        container_archive = bc.get('builder', 'container_archive')
-        self.container_archive = bc.resolve_path(container_archive)
-        os.makedirs(self.container_archive, exist_ok=True)
-        # Deploy build tarballs relative to /var/tmp/username/beeflow by default
-        deployed_image_root = bc.get('builder', 'deployed_image_root')
-        # Make sure conf_file path exists
-        os.makedirs(deployed_image_root, exist_ok=True)
-        # Make sure path is absolute
-        deployed_image_root = bc.resolve_path(deployed_image_root)
-        self.deployed_image_root = deployed_image_root
-        os.makedirs(self.deployed_image_root, exist_ok=True)
-        # Set container-relative output directory based on BeeConfig, or use '/'
-        container_output_path = bc.get('builder', 'container_output_path')
-        self.container_output_path = container_output_path
-        # record that a Charliecloud builder was used
-        # bc.modify_section('user', 'builder', {'container_type': 'charliecloud'})
-        self.task = task
-        self.docker_image_id = None
-        self.container_name = None
-        docker_requirements = set()
-        try:
-            requirement_docker_requirements = self.task.requirements['DockerRequirement'].keys()
-            docker_requirements = docker_requirements.union(requirement_docker_requirements)
-            req_string = f'{set(requirement_docker_requirements)}'
-            log.info(f'task {self.task.id} requirement DockerRequirements: {req_string}')
-        except (TypeError, KeyError):
-            log.info(f'task {self.task.name} {self.task.id} no DockerRequirements in requirement')
-        try:
-            hint_docker_requirements = self.task.hints['DockerRequirement'].keys()
-            docker_requirements = docker_requirements.union(hint_docker_requirements)
-            hint_str = f'{set(hint_docker_requirements)}'
-            log.info(f'task {self.task.name} {self.task.id} hint DockerRequirements: {hint_str}')
-        except (TypeError, KeyError):
-            log.info(f'task {self.task.name} {self.task.id} hints has no DockerRequirements')
-        log.info(f'task {self.task.id} union DockerRequirements : {docker_requirements}')
-        exec_superset = self.resolve_priority()
-        self.exec_list = [i for i in exec_superset if i[1] in docker_requirements]
-        log_exec_list = [i[1] for i in self.exec_list]
-        log.info(f'task {self.task.id} DockerRequirement execution order will be: {log_exec_list}')
-        log.info('Execution order pre-empts hint/requirement status.')
+        has_container = task.get_full_requirement('DockerRequirement')
+        if has_container:  # only try to build if task has a container
+            # Store build container archive pased on config file or relative to bee_workdir
+            # if not set.
+            container_archive = bc.get('builder', 'container_archive')
+            self.container_archive = bc.resolve_path(container_archive)
+            os.makedirs(self.container_archive, exist_ok=True)
+            # Deploy build tarballs relative to /var/tmp/username/beeflow by default
+            deployed_image_root = bc.get('builder', 'deployed_image_root')
+            # Make sure conf_file path exists
+            os.makedirs(deployed_image_root, exist_ok=True)
+            # Make sure path is absolute
+            deployed_image_root = bc.resolve_path(deployed_image_root)
+            self.deployed_image_root = deployed_image_root
+            os.makedirs(self.deployed_image_root, exist_ok=True)
+            # Set container-relative output directory based on BeeConfig, or use '/'
+            container_output_path = bc.get('builder', 'container_output_path')
+            self.container_output_path = container_output_path
+            # record that a Charliecloud builder was used
+            # bc.modify_section('user', 'builder', {'container_type': 'charliecloud'})
+            self.task = task
+            self.docker_image_id = None
+            self.container_name = None
+            docker_requirements = set()
+            try:
+                req_docker_requirements = self.task.requirements['DockerRequirement'].keys()
+                docker_requirements = docker_requirements.union(req_docker_requirements)
+                req_string = f'{set(req_docker_requirements)}'
+                log.info(f'task {self.task.id} requirement DockerRequirements: {req_string}')
+            except (TypeError, KeyError):
+                log.info(f'task {self.task.name} {self.task.id} '
+                         'no DockerRequirements in requirement')
+            try:
+                hint_docker_requirements = self.task.hints['DockerRequirement'].keys()
+                docker_requirements = docker_requirements.union(hint_docker_requirements)
+                hint_str = f'{set(hint_docker_requirements)}'
+                log.info(f'task {self.task.name} {self.task.id} hint '
+                         f'DockerRequirements: {hint_str}')
+            except (TypeError, KeyError):
+                log.info(f'task {self.task.name} {self.task.id} hints has no DockerRequirements')
+            log.info(f'task {self.task.id} union DockerRequirements : {docker_requirements}')
+            exec_superset = self.resolve_priority()
+            self.exec_list = [i for i in exec_superset if i[1] in docker_requirements]
+            log_exec_list = [i[1] for i in self.exec_list]
+            log.info(f'task {self.task.id} DockerRequirement execution order '
+                     f'will be: {log_exec_list}')
+            log.info('Execution order pre-empts hint/requirement status.')
 
     def get_docker_req(self, docker_req_param):
         """Get dockerRequirement, prioritizing requirements over hints.

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/common/config_driver.py

@@ -314,6 +314,55 @@ VALIDATOR.option('job', 'default_qos', validator=lambda val: val.strip(), prompt
 VALIDATOR.option('job', 'default_reservation', validator=lambda val: val.strip(), prompt=True,
                  default='', info='default reservation to run jobs on (leave blank if none)')
 
+def validate_attributes(val):
+    """Ensures the atributes are stored as a comma-separated string in"""
+    if isinstance(val, str):
+        parts = [p.strip() for p in val.split(',') if p.strip()]
+    elif isinstance(val, (list, tuple)):
+        parts = [str(v).strip() for v in val if str(v).strip()]
+    else:
+        raise ValueError("Expected a comma-separated string or list of strings.")
+    return ",".join(parts)
+
+slurm_command_attr= [
+        "Account","AccrueTime","CPUs_Task","Command","EligibleTime",
+        "EndTime","ExitCode","JobId","JobName","JobState",
+        "NodeList","NumCPUs","NumNodes","NumTasks","Partition",
+        "Priority","QOS","Reason","RunTime","StartTime","StdErr",
+        "StdIn","StdOut","SubmitTime","TimeLimit","UserId"
+    ]
+
+slurm_attr = [
+        "account","accrue_time","allocating_node","cluster",
+        "command","eligible_time","end_time","exit_code_number",
+        "failed_node","job_id","job_state","name","nodes",
+        "partition","qos","scheduled_nodes","standard_error",
+        "standard_input","standard_output","start_time",
+        "submit_time","tres_alloc_str"
+   ]
+
+flux_attr = [
+    "t_submit", "t_run", "t_inactive", "t_remaining","runtime",
+    "name", "id", "queue", "ntasks", "ncores", "nnodes", "nodelist","status",
+    "waitstatus", "returncode"
+]
+
+#Job attributes
+VALIDATOR.section('slurm attributes',info='Available task information for the slurm scheduler\n',
+        depends_on=('slurm', 'use_commands', 'False'))
+VALIDATOR.option('slurm attributes','attributes',validator=validate_attributes,prompt=False,
+        default='partition,nodes',info='Enter task attributes (comma-separated)')
+
+VALIDATOR.section('slurm command attributes',info='Available task information for sacct\n',
+        depends_on=('slurm', 'use_commands', 'True'))
+VALIDATOR.option('slurm command attributes','attributes',validator=validate_attributes,
+        prompt=False,default='Partition,RunTime,NodeList',
+        info='Enter task attributes (comma-separated)')
+
+VALIDATOR.section('flux attributes', info = 'Available task information for the flux scheduler\n',
+        depends_on=('DEFAULT', 'workload_scheduler', 'Flux'))
+VALIDATOR.option('flux attributes','attributes',validator=validate_attributes,prompt=False,
+        default='queue,runtime,nodelist',info='Enter task attributes (comma-separated).')
 
 def validate_chrun_opts(opts):
     """Ensure that chrun_opts don't contain options that'll conflict with BEE."""
@@ -387,8 +436,9 @@ class ConfigGenerator:
         self.validator = validator
         self.sections = {}
 
-    def choose_values(self, interactive=False, flux=False):
+    def choose_values(self, interactive=False, flux=False, attributes=False):
         """Choose configuration values based on user input."""
+        print("[DEBUG] choose_values() started")
         dirname = os.path.dirname(self.fname)
         if dirname:
             os.makedirs(dirname, exist_ok=True)
@@ -420,6 +470,20 @@ class ConfigGenerator:
                 if flux is True and opt_name == 'workload_scheduler':
                     this_default = "Flux"
                     option.prompt = False
+                if attributes and not interactive and opt_name == 'attributes':
+                    print(f'\nAvailable attributes for [{sec_name}]:')
+                    if sec_name == 'slurm attributes':
+                        attr_list = slurm_attr
+                    elif sec_name =='slurm command attributes':
+                        attr_list = slurm_command_attr
+                    else:
+                        attr_list = flux_attr
+                    print(attr_list)
+                    value = self._input_loop(opt_name, option)
+                    validated = option.validate(value)
+                    self.sections[sec_name][opt_name] = validated
+                    continue
+
                 # Check for a default value
                 if (not interactive or option.prompt is False) and this_default is not None:
                     value = option.validate(this_default)
@@ -455,7 +519,7 @@ class ConfigGenerator:
                 value = None
         return value
 
-    def save(self, interactive=False):
+    def save(self, interactive=False,attributes=False):
         """Save the config to a file."""
         print()
         print('The following configuration options were chosen:')
@@ -465,7 +529,7 @@ class ConfigGenerator:
             for opt_name in section:
                 print(f'{opt_name} = {section[opt_name]}')
         print()
-        if interactive:
+        if interactive or attributes:
             ans = input('Would you like to save this config? [y/n] ')
             if ans.lower() != 'y':
                 print('Quitting without saving')
@@ -530,12 +594,12 @@ class AlterConfig:
         for option_name, option in options:
             if option_name == opt_name:
                 # Validate the new value before changing
-                option.validate(new_value)
-                self.config[sec_name][opt_name] = new_value
+                validated = option.validate(new_value)
+                self.config[sec_name][opt_name] = validated
                 # Track changes in attribute
                 if sec_name not in self.changes:
                     self.changes[sec_name] = {}
-                self.changes[sec_name][opt_name] = new_value
+                self.changes[sec_name][opt_name] = validated
                 return
 
         raise ValueError(f'Option {opt_name} not found in the validator for section {sec_name}.')
@@ -590,10 +654,12 @@ def info():
 def new(path: str = typer.Argument(default=USERCONFIG_FILE,
                                    help='Path to new config file'),
         interactive: bool = typer.Option(False, '--interactive', '-i',
-                                         help='Whether or not to be prompted'
-                                         + ' during config generation'),
+                                         help='Interactive session to generate config'),
         flux: bool = typer.Option(False, '--flux', '-f',
-                                  help='Changes default scheduler to Flux')):
+                                  help='Changes default scheduler to Flux'),
+        attributes: bool = typer.Option(False, '--attributes', '-a',
+                                        help='Chooses task attributes to display'
+                                        'for "beeflow query"')):
     """Create a new config file."""
     if os.path.exists(path):
         if not interactive or check_yes(f'Path "{path}" already exists.\n'
@@ -601,8 +667,9 @@ def new(path: str = typer.Argument(default=USERCONFIG_FILE,
             config_utils.backup(path)
     ConfigGenerator(path, VALIDATOR).choose_values(
         flux=flux,
-        interactive=interactive
-    ).save(interactive=interactive)
+        interactive=interactive,
+        attributes=attributes
+    ).save(interactive=interactive,attributes=attributes)
 
 
 @app.command()

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/common/config_utils.py

@@ -25,6 +25,8 @@ def write_config(file_name, sections):
                 print(file=fp)
                 print(f'[{sec_name}]', file=fp)
                 for opt_name, value in section.items():
+                    if isinstance(value, (list, tuple)):
+                        value = ",".join(str(v).strip() for v in value if str(v).strip())
                     print(f'{opt_name} = {value}', file=fp)
     except FileNotFoundError:
         print('Configuration file does not exist!')

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/common/config_validator.py

@@ -92,8 +92,10 @@ class ConfigValidator:
             return True
         if depends_on[0] not in conf or depends_on[1] not in conf[depends_on[0]]:
             return False
+        actual=str(conf[depends_on[0]][depends_on[1]])
+        expected=str(depends_on[2])
         # Value must match for the section to be valid
-        return conf[depends_on[0]][depends_on[1]] == depends_on[2]
+        return actual.strip().lower()==expected.strip().lower()
 
     def is_section_valid(self, cur_conf, sec_name):
         """Determine if given the current configuration, sec_name is valid.

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/common/cwl/cwl.py

@@ -621,9 +621,8 @@ class CWL:
         self.steps = steps
 
     def dump_wf(self, path=None):
-        """Dump the workflow. If no path is specified print to stdout."""
+        """Dump the workflow. If no path is specified return cwl file as a string."""
         cwl_dump = ruamel.yaml.comments.CommentedMap()
-        # cwl_dump = {}
         cwl_dump.update(self.header.dump())
         cwl_dump.update(self.header.dump())
         cwl_dump.update(self.inputs.dump())
@@ -638,12 +637,10 @@ class CWL:
         if path:
             with open(f"{path}/{self.cwl_name}.cwl", "w", encoding="utf-8") as wf_file:
                 print(wf_contents, file=wf_file)
-        else:
-            print(wf_contents)
         return wf_contents
 
     def dump_inputs(self, path=None):
-        """Dump YAML inputs."""
+        """Dump YAML inputs. If no path is specified return yaml file as a string."""
         stream = StringIO()
         yaml.dump(self.inputs.generate_yaml_inputs(), stream)
         yaml_contents = stream.getvalue()

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/common/cwl/examples/cat_grep_tar.py

@@ -40,8 +40,8 @@ def main():
                         source="tar/tarball")])
 
     workflow = Workflow("cat-grep-tar", [cat, grep0, grep1, tar])
-    workflow.write_wf("cat-grep-tar")
-    workflow.write_yaml("cat-grep-tar")
+    workflow.dump_wf("cat-grep-tar")
+    workflow.dump_yaml("cat-grep-tar")
 
 
 if __name__ == "__main__":

{hpc_beeflow-0.1.11.dev2 → hpc_beeflow-0.1.11.dev4}/beeflow/common/cwl/examples/comd.py

@@ -30,19 +30,15 @@ def main():
                         # The slurm requirement
                         MPI(nodes=4, ntasks=8),
                         # Example of slurm options
-                        # Slurm(account="standard", time_limit=60, partition="standard",
-                        #      qos="debug", reservation="standard"),
+                        Slurm(account="standard", time_limit=60, partition="standard",
+                              qos="debug", reservation="standard"),
                         Script(pre_script="comd_pre.sh"),
-                        Slurm(time_limit="500"),
                         Charliecloud(docker_file="Dockerfile.comd-x86_64",
                                      container_name="comd-mpi")
                      ])
     workflow = Workflow("comd", [comd_task])
-    workflow.write_wf("comd")
-    workflow.write_yaml("comd")
-    # workflow = Workflow("comd", [comd_task])
-    # workflow.write(".")
-
+    workflow.dump_wf("comd")
+    workflow.dump_yaml("comd")
 
 if __name__ == "__main__":
     main()